Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 12 22:54:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/08_2023/7nxd_12637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/08_2023/7nxd_12637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/08_2023/7nxd_12637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/08_2023/7nxd_12637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/08_2023/7nxd_12637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nxd_12637/08_2023/7nxd_12637.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Mg 1 5.21 5 S 94 5.16 5 C 7948 2.51 5 N 2142 2.21 5 O 2613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 24": "OE1" <-> "OE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 540": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A TYR 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 6": "NH1" <-> "NH2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 90": "OD1" <-> "OD2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 226": "OD1" <-> "OD2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 327": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B ARG 475": "NH1" <-> "NH2" Residue "B ARG 478": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 12805 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 6953 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 58, 'TRANS': 846} Chain breaks: 2 Chain: "B" Number of atoms: 5314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5314 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 25, 'TRANS': 664} Chain breaks: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 19 Unusual residues: {' CA': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" N ALA A 784 " occ=0.66 ... (3 atoms not shown) pdb=" CB ALA A 784 " occ=0.66 residue: pdb=" N TYR A 789 " occ=0.66 ... (10 atoms not shown) pdb=" OH TYR A 789 " occ=0.66 residue: pdb=" N GLU A 790 " occ=0.66 ... (7 atoms not shown) pdb=" OE2 GLU A 790 " occ=0.66 residue: pdb=" N LEU A 882 " occ=0.66 ... (6 atoms not shown) pdb=" CD2 LEU A 882 " occ=0.66 residue: pdb=" N TRP A 900 " occ=0.66 ... (12 atoms not shown) pdb=" CH2 TRP A 900 " occ=0.66 residue: pdb=" N PRO A 926 " occ=0.66 ... (5 atoms not shown) pdb=" CD PRO A 926 " occ=0.66 residue: pdb=" N TYR A 927 " occ=0.66 ... (10 atoms not shown) pdb=" OH TYR A 927 " occ=0.66 residue: pdb=" N GLY B 618 " occ=0.75 ... (2 atoms not shown) pdb=" O GLY B 618 " occ=0.75 residue: pdb=" N CYS B 620 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 620 " occ=0.75 residue: pdb=" N LYS B 624 " occ=0.75 ... (7 atoms not shown) pdb=" NZ LYS B 624 " occ=0.75 residue: pdb=" N GLU B 625 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU B 625 " occ=0.75 residue: pdb=" N CYS B 626 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS B 626 " occ=0.75 ... (remaining 16 not shown) Time building chain proxies: 6.60, per 1000 atoms: 0.52 Number of scatterers: 12805 At special positions: 0 Unit cell: (104.55, 136, 168.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 7 19.99 S 94 16.00 Mg 1 11.99 O 2613 8.00 N 2142 7.00 C 7948 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 481 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 543 " distance=2.03 Simple disulfide: pdb=" SG CYS A 604 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 690 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 916 " distance=2.03 Simple disulfide: pdb=" SG CYS A 828 " - pdb=" SG CYS A 880 " distance=2.03 Simple disulfide: pdb=" SG CYS A 870 " - pdb=" SG CYS A 875 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 444 " distance=2.04 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 44 " distance=2.03 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 281 " distance=1.83 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 395 " distance=2.30 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 442 " distance=1.92 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 457 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 480 " distance=2.03 Simple disulfide: pdb=" SG CYS B 482 " - pdb=" SG CYS B 513 " distance=2.02 Simple disulfide: pdb=" SG CYS B 496 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS B 540 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 548 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 561 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 595 " distance=2.03 Simple disulfide: pdb=" SG CYS B 579 " - pdb=" SG CYS B 593 " distance=2.02 Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 598 " distance=2.04 Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 610 " distance=2.04 Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 616 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 645 " distance=2.04 Simple disulfide: pdb=" SG CYS B 629 " - pdb=" SG CYS B 641 " distance=2.04 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 703 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 6 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " BETA1-2 " MAN G 4 " - " NAG G 5 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A1106 " - " ASN A 483 " " NAG C 1 " - " ASN A 43 " " NAG D 1 " - " ASN A 141 " " NAG E 1 " - " ASN A 256 " " NAG F 1 " - " ASN A 266 " " NAG G 1 " - " ASN A 275 " " NAG H 1 " - " ASN A 568 " " NAG I 1 " - " ASN A 489 " " NAG J 1 " - " ASN B 192 " " NAG K 1 " - " ASN B 249 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 386 " " NAG N 1 " - " ASN B 397 " " NAG O 1 " - " ASN B 461 " " NAG P 1 " - " ASN B 30 " Time building additional restraints: 6.15 Conformation dependent library (CDL) restraints added in 1.8 seconds 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2900 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 29 sheets defined 12.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 184 through 189 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 223 through 227 Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 509 through 512 Processing helix chain 'A' and resid 869 through 873 Processing helix chain 'A' and resid 900 through 907 removed outlier: 3.731A pdb=" N ARG A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 14 through 22 removed outlier: 3.702A pdb=" N CYS B 18 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 19 " --> pdb=" O CYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 42 Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.590A pdb=" N GLY B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 135 through 157 removed outlier: 3.509A pdb=" N ASN B 141 " --> pdb=" O ASP B 137 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N THR B 147 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 155 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 removed outlier: 3.813A pdb=" N ASN B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 removed outlier: 4.040A pdb=" N PHE B 212 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.705A pdb=" N ALA B 234 " --> pdb=" O GLY B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 321 through 332 removed outlier: 3.834A pdb=" N ASN B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'B' and resid 389 through 393 Processing helix chain 'B' and resid 444 through 450 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 546 through 551 removed outlier: 3.503A pdb=" N GLY B 549 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.728A pdb=" N SER A 437 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 418 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 26 removed outlier: 4.025A pdb=" N TYR A 26 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER A 34 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL A 55 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 95 removed outlier: 4.093A pdb=" N SER A 120 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 4.061A pdb=" N THR A 139 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG A 144 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.580A pdb=" N SER A 169 " --> pdb=" O GLY A 181 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 217 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.106A pdb=" N SER A 234 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 274 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ASN A 266 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER A 272 " --> pdb=" O ASN A 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 288 through 292 removed outlier: 3.578A pdb=" N ALA A 288 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 326 " --> pdb=" O LEU A 340 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 340 " --> pdb=" O VAL A 326 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.637A pdb=" N GLN A 319 " --> pdb=" O ASP A 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.780A pdb=" N VAL A 369 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 384 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 402 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 386 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 519 through 521 removed outlier: 3.510A pdb=" N LEU A 488 " --> pdb=" O ASP A 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 544 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 486 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER A 485 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 459 " --> pdb=" O SER A 485 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 489 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 491 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 498 through 499 Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AB4, first strand: chain 'A' and resid 529 through 532 Processing sheet with id=AB5, first strand: chain 'A' and resid 614 through 621 removed outlier: 3.555A pdb=" N GLU A 621 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASN A 634 " --> pdb=" O GLU A 621 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 664 " --> pdb=" O ARG A 707 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N THR A 709 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 662 " --> pdb=" O THR A 709 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 677 through 680 removed outlier: 3.743A pdb=" N LEU A 687 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU A 688 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA A 650 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A 725 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP A 723 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 751 through 757 removed outlier: 6.304A pdb=" N GLN A 894 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 823 " --> pdb=" O GLN A 894 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS A 896 " --> pdb=" O THR A 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 828 through 830 removed outlier: 3.655A pdb=" N LEU A 804 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN A 801 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 923 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 866 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN A 915 " --> pdb=" O GLN A 866 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 868 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N GLU A 917 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 828 through 830 removed outlier: 3.655A pdb=" N LEU A 804 " --> pdb=" O CYS A 880 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN A 801 " --> pdb=" O LEU A 923 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 923 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AC2, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.060A pdb=" N LEU B 99 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 423 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.654A pdb=" N GLN B 109 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 109 through 111 removed outlier: 3.654A pdb=" N GLN B 109 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 199 through 201 removed outlier: 7.062A pdb=" N ILE B 123 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLY B 163 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 125 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B 165 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR B 127 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE B 167 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N MET B 129 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASP B 124 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 255 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 126 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N SER B 257 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 128 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 258 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL B 317 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 362 through 363 Processing sheet with id=AC7, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AC8, first strand: chain 'B' and resid 509 through 512 removed outlier: 3.514A pdb=" N VAL B 517 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 512 " --> pdb=" O GLN B 515 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AD1, first strand: chain 'B' and resid 592 through 594 removed outlier: 3.898A pdb=" N GLU B 594 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 671 through 674 removed outlier: 3.590A pdb=" N PHE B 683 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 673 " --> pdb=" O PHE B 681 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.67 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2648 1.33 - 1.45: 3073 1.45 - 1.58: 7218 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 13051 Sorted by residual: bond pdb=" N CYS B 415 " pdb=" CA CYS B 415 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.10e-03 1.21e+04 1.51e+01 bond pdb=" N GLU A 126 " pdb=" CA GLU A 126 " ideal model delta sigma weight residual 1.453 1.488 -0.035 9.20e-03 1.18e+04 1.44e+01 bond pdb=" N LYS B 87 " pdb=" CA LYS B 87 " ideal model delta sigma weight residual 1.456 1.488 -0.033 8.70e-03 1.32e+04 1.40e+01 bond pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.17e-02 7.31e+03 1.30e+01 bond pdb=" N VAL A 756 " pdb=" CA VAL A 756 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.11e-02 8.12e+03 1.29e+01 ... (remaining 13046 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.74: 430 106.74 - 113.64: 7216 113.64 - 120.54: 5568 120.54 - 127.43: 4400 127.43 - 134.33: 64 Bond angle restraints: 17678 Sorted by residual: angle pdb=" CA GLY B 607 " pdb=" C GLY B 607 " pdb=" O GLY B 607 " ideal model delta sigma weight residual 122.37 118.05 4.32 7.30e-01 1.88e+00 3.51e+01 angle pdb=" C ARG A 350 " pdb=" N PHE A 351 " pdb=" CA PHE A 351 " ideal model delta sigma weight residual 120.75 129.43 -8.68 1.51e+00 4.39e-01 3.30e+01 angle pdb=" CA GLY B 530 " pdb=" C GLY B 530 " pdb=" O GLY B 530 " ideal model delta sigma weight residual 122.23 118.56 3.67 6.90e-01 2.10e+00 2.83e+01 angle pdb=" C LEU A 79 " pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 122.30 115.21 7.09 1.35e+00 5.49e-01 2.76e+01 angle pdb=" CA GLY B 81 " pdb=" C GLY B 81 " pdb=" O GLY B 81 " ideal model delta sigma weight residual 122.23 118.66 3.57 6.90e-01 2.10e+00 2.68e+01 ... (remaining 17673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 7247 17.99 - 35.99: 313 35.99 - 53.98: 55 53.98 - 71.97: 15 71.97 - 89.97: 7 Dihedral angle restraints: 7637 sinusoidal: 3093 harmonic: 4544 Sorted by residual: dihedral pdb=" CB CYS B 457 " pdb=" SG CYS B 457 " pdb=" SG CYS B 469 " pdb=" CB CYS B 469 " ideal model delta sinusoidal sigma weight residual -86.00 -175.97 89.97 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS A 472 " pdb=" SG CYS A 472 " pdb=" SG CYS A 481 " pdb=" CB CYS A 481 " ideal model delta sinusoidal sigma weight residual -86.00 -170.83 84.83 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual -86.00 -165.52 79.52 1 1.00e+01 1.00e-02 7.85e+01 ... (remaining 7634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.169: 1817 0.169 - 0.337: 213 0.337 - 0.506: 6 0.506 - 0.674: 0 0.674 - 0.843: 1 Chirality restraints: 2037 Sorted by residual: chirality pdb=" C1 MAN D 4 " pdb=" O3 BMA D 3 " pdb=" C2 MAN D 4 " pdb=" O5 MAN D 4 " both_signs ideal model delta sigma weight residual False 2.40 1.56 0.84 2.00e-02 2.50e+03 1.78e+03 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.48e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-02 2.50e+03 1.66e+02 ... (remaining 2034 not shown) Planarity restraints: 2310 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG O 1 " -0.360 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG O 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG O 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG O 1 " 0.551 2.00e-02 2.50e+03 pdb=" O7 NAG O 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.351 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG G 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.099 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.15e+03 pdb=" C7 NAG E 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.150 2.00e-02 2.50e+03 ... (remaining 2307 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 101 2.44 - 3.06: 9052 3.06 - 3.67: 18096 3.67 - 4.29: 26307 4.29 - 4.90: 43308 Nonbonded interactions: 96864 Sorted by model distance: nonbonded pdb=" O SER B 134 " pdb="CA CA B1002 " model vdw 1.831 2.510 nonbonded pdb=" OD1 ASP A 243 " pdb="CA CA A1101 " model vdw 1.885 2.510 nonbonded pdb=" OG SER A 241 " pdb="CA CA A1101 " model vdw 1.904 2.510 nonbonded pdb=" OD1 ASN A 428 " pdb="CA CA A1104 " model vdw 1.914 2.510 nonbonded pdb=" OD2 ASP B 226 " pdb="CA CA B1003 " model vdw 2.011 2.510 ... (remaining 96859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'M' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.880 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 37.140 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4646 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.050 13051 Z= 0.888 Angle : 1.509 8.678 17678 Z= 1.119 Chirality : 0.108 0.843 2037 Planarity : 0.029 0.310 2295 Dihedral : 9.251 74.975 4626 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 64.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.20), residues: 1583 helix: 1.10 (0.49), residues: 132 sheet: -0.17 (0.24), residues: 460 loop : -1.21 (0.18), residues: 991 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 193 average time/residue: 0.3082 time to fit residues: 80.9477 Evaluate side-chains 98 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.469 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1323 time to fit residues: 3.0450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 165 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS A 587 HIS A 787 HIS A 801 GLN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN B 74 ASN B 77 ASN B 93 GLN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 623 HIS B 628 GLN ** B 633 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 670 HIS ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4992 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 13051 Z= 0.335 Angle : 0.930 12.282 17678 Z= 0.449 Chirality : 0.056 0.606 2037 Planarity : 0.005 0.077 2295 Dihedral : 4.516 17.935 1712 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.20), residues: 1583 helix: 0.36 (0.39), residues: 149 sheet: 0.00 (0.23), residues: 490 loop : -0.95 (0.19), residues: 944 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.2958 time to fit residues: 46.6274 Evaluate side-chains 74 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.397 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 128 optimal weight: 40.0000 chunk 143 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS A 816 GLN ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN B 322 GLN B 349 GLN ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 ASN ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5070 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 13051 Z= 0.266 Angle : 0.762 9.460 17678 Z= 0.376 Chirality : 0.051 0.434 2037 Planarity : 0.005 0.077 2295 Dihedral : 4.560 21.674 1712 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1583 helix: 0.42 (0.41), residues: 150 sheet: 0.11 (0.23), residues: 495 loop : -0.86 (0.19), residues: 938 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.3047 time to fit residues: 38.1620 Evaluate side-chains 60 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5105 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 13051 Z= 0.219 Angle : 0.705 10.434 17678 Z= 0.340 Chirality : 0.049 0.458 2037 Planarity : 0.004 0.063 2295 Dihedral : 4.560 22.671 1712 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1583 helix: 0.65 (0.42), residues: 152 sheet: 0.13 (0.22), residues: 500 loop : -0.79 (0.19), residues: 931 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3112 time to fit residues: 34.4840 Evaluate side-chains 57 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 1.472 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 131 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 HIS ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 GLN ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5432 moved from start: 0.7303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.083 13051 Z= 0.499 Angle : 1.049 16.281 17678 Z= 0.533 Chirality : 0.057 0.624 2037 Planarity : 0.007 0.081 2295 Dihedral : 6.265 33.849 1712 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 45.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1583 helix: -0.96 (0.38), residues: 150 sheet: -0.27 (0.22), residues: 492 loop : -1.21 (0.19), residues: 941 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 64 average time/residue: 0.2856 time to fit residues: 27.3507 Evaluate side-chains 42 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 0.4980 chunk 30 optimal weight: 20.0000 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 HIS ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5272 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 13051 Z= 0.220 Angle : 0.738 11.310 17678 Z= 0.360 Chirality : 0.050 0.490 2037 Planarity : 0.004 0.058 2295 Dihedral : 5.398 27.432 1712 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1583 helix: -0.43 (0.40), residues: 150 sheet: -0.19 (0.22), residues: 515 loop : -1.04 (0.20), residues: 918 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.2845 time to fit residues: 26.6858 Evaluate side-chains 47 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.508 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5267 moved from start: 0.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13051 Z= 0.203 Angle : 0.696 9.772 17678 Z= 0.337 Chirality : 0.048 0.479 2037 Planarity : 0.004 0.056 2295 Dihedral : 5.072 25.713 1712 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.20), residues: 1583 helix: -0.42 (0.40), residues: 153 sheet: -0.08 (0.22), residues: 523 loop : -0.93 (0.20), residues: 907 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2478 time to fit residues: 22.9288 Evaluate side-chains 47 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 1.410 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 20.0000 chunk 46 optimal weight: 0.6980 chunk 30 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 120 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 HIS A 891 GLN ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 940 GLN B 628 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5188 moved from start: 0.7504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 13051 Z= 0.169 Angle : 0.672 9.626 17678 Z= 0.321 Chirality : 0.048 0.428 2037 Planarity : 0.004 0.054 2295 Dihedral : 4.823 23.974 1712 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1583 helix: -0.11 (0.42), residues: 154 sheet: 0.05 (0.22), residues: 513 loop : -0.87 (0.20), residues: 916 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2743 time to fit residues: 26.6974 Evaluate side-chains 49 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 93 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 HIS B 98 GLN ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 0.8523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 13051 Z= 0.312 Angle : 0.821 11.729 17678 Z= 0.405 Chirality : 0.050 0.434 2037 Planarity : 0.005 0.058 2295 Dihedral : 5.550 30.098 1712 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 35.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1583 helix: -0.77 (0.38), residues: 156 sheet: -0.13 (0.23), residues: 488 loop : -1.02 (0.20), residues: 939 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2821 time to fit residues: 24.2265 Evaluate side-chains 42 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 overall best weight: 5.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 HIS ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN A 786 HIS ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5400 moved from start: 0.9169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 13051 Z= 0.274 Angle : 0.773 11.374 17678 Z= 0.381 Chirality : 0.049 0.462 2037 Planarity : 0.005 0.059 2295 Dihedral : 5.718 35.506 1712 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 33.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.20), residues: 1583 helix: -1.07 (0.37), residues: 161 sheet: -0.41 (0.22), residues: 488 loop : -1.07 (0.20), residues: 934 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3166 Ramachandran restraints generated. 1583 Oldfield, 0 Emsley, 1583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2559 time to fit residues: 21.6951 Evaluate side-chains 41 residues out of total 1362 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.483 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 126 optimal weight: 30.0000 chunk 52 optimal weight: 20.0000 chunk 129 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 GLN ** A 886 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.061505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.040512 restraints weight = 136850.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.040512 restraints weight = 129915.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.040512 restraints weight = 129916.079| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 82 | |-----------------------------------------------------------------------------| r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.9719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 13051 Z= 0.296 Angle : 0.790 11.244 17678 Z= 0.392 Chirality : 0.050 0.480 2037 Planarity : 0.005 0.060 2295 Dihedral : 5.884 38.986 1712 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 36.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.20), residues: 1583 helix: -1.33 (0.36), residues: 168 sheet: -0.55 (0.22), residues: 505 loop : -1.18 (0.20), residues: 910 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.59 seconds wall clock time: 42 minutes 54.71 seconds (2574.71 seconds total)